I have found a similar question at Calculate Rotation Matrix to align k n dimensional vectors but not quite the same what I want to do.
Problem:
$S_1, S_2 \in \Re^{D \times d} $ where ${D > d} $ and columns of each matrix are orthonormal. Need to find a $R \in \Re^{D \times D}$ orthonormal rotation matrix such that $Col(S_2) \equiv Col(R S_1)$ where $Col(\cdot)$ represents the column space.
Any insight towards a solution is much appreciated.